[English] 日本語
Yorodumi
- PDB-7s3e: Solution NMR structure of uperin 3.5 in SDS micelles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s3e
TitleSolution NMR structure of uperin 3.5 in SDS micelles
ComponentsUperin-3.5
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homologyUperin / Uperin family / cytolysis in another organism / other organism cell membrane / defense response to Gram-positive bacterium / protein homodimerization activity / extracellular region / membrane / Uperin-3.5
Function and homology information
Biological speciesUperoleia mjobergii (Mjoberg's toadlet)
MethodSOLUTION NMR / simulated annealing
AuthorsRosengren, K.J. / Armstrong, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Structural insight into the mechanisms underlying the membrane activity of a family of antimicrobial Uperin 3 peptides
Authors: Prasad, A.K. / Tiwari, C. / Ray, S. / Holden, S. / Armstrong, D.A. / Rosengren, K.J. / Rodger, A. / Martin, L.L. / Panwar, A.S.
History
DepositionSep 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uperin-3.5


Theoretical massNumber of molelcules
Total (without water)1,7821
Polymers1,7821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NOE data fully consistent with monomeric structure
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint1 kcal/mol
Surface area1830 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Uperin-3.5


Mass: 1782.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Uperoleia mjobergii (Mjoberg's toadlet) / References: UniProt: P82042
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HSQC

-
Sample preparation

DetailsType: solution
Contents: 2 mg/mL uperin 3.5, 100 mM [U-100% 2H] SDS, 90% H2O/10% D2O
Label: SDS micelle sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLuperin 3.5natural abundance1
100 mMSDS[U-100% 2H]1
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 5.25 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: equipped with cryoprobe

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more